fhach
commented
3 years ago @nedoluzhko, this should have been fixed in the latest commit.
Closed nedoluzhko closed 3 years ago
fhach
commented
3 years ago @nedoluzhko, this should have been fixed in the latest commit.
Hello, thank you for your tool. But I have a small problem after genome indexing. Can you help me? I suppose that the problem with GTF file. I tried to use Danio rerio GTF annotation file from Ensembl.
Artem
circminer -r drerio.fa -g Danio_rerio.GRCz11.100.gtf -1 1.fq -2 2.fq -o output Fri Jul 10 15:13:07 2020 [INFO] Number of threads: 1 Fri Jul 10 15:13:07 2020 [INFO] Input file type: Paired-end Fri Jul 10 15:13:08 2020 [INFO] Kmer size obtained from index: 20 Fri Jul 10 15:13:08 2020 [INFO] Loading GTF file... Fri Jul 10 15:13:13 2020 [INFO] {GTFParser} WARNING: Gene annotation file does not contain any records of some contigs. Fri Jul 10 15:13:13 2020 [INFO] Completed! (CPU time: 5.95s; Real time: 5.96s) Fri Jul 10 15:13:13 2020 [INFO] Genome index type: Full Fri Jul 10 15:13:13 2020 [INFO] Starting read extraction Fri Jul 10 15:13:13 2020 [INFO] + Loading genome index... Fri Jul 10 15:13:24 2020 [INFO] + Completed! (CPU time: 10.59s; Real time: 10.61s) Fri Jul 10 15:13:24 2020 [INFO] + Loading genome sequence... Fri Jul 10 15:13:25 2020 [INFO] + Completed! (CPU time: 1.90s; Real time: 1.90s) Fri Jul 10 15:13:25 2020 [INFO] + Starting pseudo-alignment (Round 1) Segmentation fault (core dumped)